Contacts of the helix formed by residues 346 - 368 (chain C) in PDB entry 4P3N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 346 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLU* 3.6 49.4 - - + +
332C LEU 3.0 11.3 + - - +
333C TYR* 4.7 2.2 - - - +
334C PHE* 3.9 37.0 - - + -
344C PHE 3.7 0.4 + - - -
345C PHE* 1.3 74.0 - - - +
347C PRO* 1.4 82.1 - - + +
348C LYS 3.2 0.9 - - - -
349C GLY 3.0 2.8 + - - -
350C ALA* 2.8 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE 4.8 0.4 - - - +
346C LEU* 1.4 93.8 - - + +
348C LYS* 1.3 62.1 + - + +
350C ALA* 3.3 8.5 + - + +
351C TYR* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C GLN 4.2 1.6 - - - +
331C GLU* 3.8 19.2 + - + +
332C LEU* 3.8 7.2 - - + -
346C LEU 3.2 1.0 - - - -
347C PRO* 1.3 81.9 - - + +
349C GLY* 1.3 63.1 + - - +
351C TYR* 3.6 7.6 - - - +
352C ILE* 3.4 7.1 - - - +
618C PRO* 3.4 43.8 - - + +
619C ARG* 3.4 53.3 - - - +
647C MET* 6.1 2.7 - - - -
649C ASP* 4.9 10.7 + - - -
670C TYR* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU* 3.5 35.5 + - - +
333C TYR* 5.1 0.4 - - - -
345C PHE* 3.9 16.9 - - - -
346C LEU 3.0 3.8 + - - -
348C LYS* 1.3 75.9 - - - +
350C ALA* 1.3 59.5 + - - +
351C TYR 3.2 0.2 - - - -
352C ILE* 3.1 10.8 + - - +
353C TYR* 2.9 26.2 + - - +
601C ILE* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 4.0 14.8 - - + +
346C LEU 2.8 12.7 + - - +
347C PRO* 3.4 13.5 - - + +
349C GLY* 1.3 77.6 - - - +
351C TYR* 1.3 61.5 - - - +
353C TYR* 3.2 9.6 - - - +
354C ASN* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C PRO 2.9 13.3 + - - +
348C LYS* 3.6 12.3 - - - +
350C ALA* 1.3 77.6 - - - +
352C ILE* 1.3 59.1 + - + +
354C ASN* 3.4 5.3 + - - +
355C ALA* 2.9 37.0 + - + +
615C TRP 3.6 18.7 + - - -
616C LEU 4.0 8.3 - - - -
617C SER 3.4 23.1 - - - -
618C PRO* 4.0 9.0 - - + -
620C GLN* 3.2 21.8 + - - -
645C LYS 5.1 4.9 + - - -
647C MET* 3.7 37.5 - - + -
712C LYS* 4.3 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU* 4.0 12.3 - - + -
333C TYR* 6.1 0.2 - - + -
348C LYS 3.4 11.9 - - - +
349C GLY* 3.1 8.4 + - - +
351C TYR* 1.3 73.3 - - + +
353C TYR* 1.3 66.2 + - - +
355C ALA* 3.2 6.4 + - - +
356C LEU* 2.9 26.3 + - + +
601C ILE* 4.1 24.2 - - + -
612C TRP* 3.6 42.8 - - + -
616C LEU* 3.5 34.5 - - + +
618C PRO* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PHE* 3.7 44.9 - + - -
349C GLY 2.9 10.6 + - - +
350C ALA* 3.2 13.9 - - - +
352C ILE* 1.3 77.9 - - - +
354C ASN* 1.3 63.8 + - - +
356C LEU* 3.2 3.3 + - - +
357C ILE* 3.0 57.9 + - + +
457C ARG* 3.3 13.6 + - - -
459C GLN* 3.4 23.0 - - - +
597C VAL* 3.8 25.9 - - + +
598C GLU* 2.8 28.8 + - - -
601C ILE* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ALA* 2.9 23.7 + - - +
351C TYR* 3.9 5.6 - - + +
353C TYR* 1.3 90.6 - - - +
355C ALA* 1.3 57.7 + - - +
357C ILE* 3.8 11.6 - - - +
358C GLU* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C TYR* 2.9 28.0 + - + +
352C ILE* 3.5 8.5 - - - +
353C TYR 3.2 0.2 - - - -
354C ASN* 1.3 75.1 - - - +
356C LEU* 1.3 59.3 + - - +
358C GLU* 3.5 6.1 + - - +
359C PHE* 2.9 27.5 + - - +
615C TRP* 4.0 23.4 - - + +
616C LEU* 4.4 11.9 - - + -
715C ARG* 5.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ILE* 2.9 19.5 + - + +
353C TYR 3.5 7.0 - - - +
355C ALA* 1.3 73.9 - - - +
357C ILE* 1.3 66.0 + - - +
359C PHE* 3.1 8.3 + - + +
360C ILE* 3.0 27.8 + - - +
490C PHE* 3.8 34.3 - - + -
594C LEU* 4.3 13.7 - - + -
597C VAL* 4.4 10.8 - - + +
600C MET* 4.4 17.5 - - + -
601C ILE* 3.6 31.4 - - + -
604C LEU* 4.3 7.2 - - + -
615C TRP* 4.2 5.4 - - + -
616C LEU* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TYR* 3.0 44.3 + - + +
354C ASN* 3.8 12.1 - - - +
356C LEU* 1.3 74.4 - - - +
358C GLU* 1.3 56.7 + - - +
360C ILE* 3.3 5.0 + - - +
361C ARG* 2.9 54.1 + - - +
437C PHE* 3.6 33.7 - - + -
459C GLN* 3.9 12.3 - - - +
594C LEU* 5.6 0.4 - - - -
597C VAL* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C ASN 2.9 19.7 + - - +
355C ALA* 3.8 6.1 - - - +
357C ILE* 1.3 73.3 - - - +
359C PHE* 1.3 61.5 + - - +
361C ARG* 4.2 15.5 + - - +
362C SER* 2.9 29.3 + - - -
365C ARG* 2.5 39.5 + - - -
715C ARG* 4.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ALA 2.9 14.7 + - - +
356C LEU* 3.3 11.2 - - + +
358C GLU* 1.3 76.1 - - - +
360C ILE* 1.3 70.4 + - + +
362C SER* 2.7 20.9 + - - -
363C GLU* 3.0 25.2 + - + +
485C THR 4.8 0.4 - - - -
486C VAL* 3.6 42.6 - - + -
489C VAL* 3.9 32.8 - - + -
490C PHE* 4.3 13.0 - + - -
615C TRP* 4.1 14.8 - + + -
715C ARG* 3.2 47.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C LEU 3.0 14.1 + - - +
357C ILE 3.6 7.2 - - - +
359C PHE* 1.3 87.6 - - + +
361C ARG* 1.3 56.0 + - - +
363C GLU* 3.2 6.7 + - - +
364C TYR* 2.9 63.6 + - + +
437C PHE* 3.7 11.4 - - + -
461C ASP* 4.0 15.0 - - + +
482C PHE* 4.9 6.1 - - + -
486C VAL* 4.6 16.8 - - + -
591C ARG* 5.5 0.2 - - - +
593C ILE* 5.2 2.9 - - + -
594C LEU* 3.5 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ILE* 2.9 35.4 + - - +
358C GLU* 3.7 18.4 + - - +
360C ILE* 1.3 72.7 - - - +
362C SER* 1.3 61.9 + - - +
364C TYR* 2.9 25.8 + - + +
365C ARG* 2.9 34.7 + - + +
371C GLU* 2.9 37.9 + - - +
437C PHE* 3.5 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C GLU* 2.9 19.4 + - - -
359C PHE 2.7 14.1 + - - -
361C ARG* 1.3 75.6 - - - +
363C GLU* 1.3 69.5 + - - +
365C ARG* 3.2 25.5 + - - +
366C LYS* 3.6 24.3 + - - +
715C ARG* 3.8 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C PHE* 3.0 22.9 + - + +
360C ILE* 3.7 6.3 - - + +
361C ARG 3.1 0.2 - - - -
362C SER* 1.3 92.1 + - - +
364C TYR* 1.3 60.4 + - - +
366C LYS* 3.1 22.4 + - - +
367C ARG* 2.9 56.7 + - - +
482C PHE* 3.5 31.4 - - + -
485C THR* 4.7 12.7 - - - +
486C VAL* 4.9 6.5 - - + -
715C ARG* 5.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 2.9 37.2 + - + +
361C ARG* 2.9 17.9 + - + +
363C GLU* 1.3 78.0 - - - +
365C ARG* 1.3 62.5 + - + +
367C ARG 4.4 0.2 - - - +
368C GLY* 3.2 6.1 + - - -
369C PHE* 3.0 58.2 + + + +
371C GLU* 5.4 5.8 - - + +
435C ALA* 3.4 26.5 - - + +
436C ASP 5.5 0.4 - - - -
437C PHE* 4.1 16.2 - + - -
461C ASP* 4.0 17.5 - - - +
462C ASP 4.1 2.4 + - - -
463C ALA* 4.1 3.6 - - + +
482C PHE* 3.5 16.6 - + - -
591C ARG* 3.3 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C GLU* 2.5 37.8 + - - -
361C ARG* 2.9 24.0 + - + +
362C SER* 3.2 33.5 + - - +
363C GLU 3.3 0.2 - - - -
364C TYR* 1.3 77.5 - - + +
366C LYS* 1.3 61.6 + - + +
368C GLY* 4.1 4.5 + - - -
369C PHE 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C SER 3.6 15.3 - - - +
363C GLU* 3.1 29.9 + - - +
365C ARG* 1.3 81.0 - - + +
367C ARG* 1.3 64.2 + - + +
368C GLY 3.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C GLU* 2.9 30.9 + - - +
364C TYR 3.3 0.8 + - - -
366C LYS* 1.3 83.1 - - + +
368C GLY* 1.3 60.9 + - - +
369C PHE* 3.5 23.0 - - + -
433C ARG* 3.8 13.0 + - - -
478C GLY* 3.9 7.9 + - - -
481C ASP* 2.5 34.7 + - - +
482C PHE* 3.4 51.9 - - - +
485C THR* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C TYR 3.2 3.2 + - - -
365C ARG 4.1 3.6 + - - -
366C LYS 3.5 4.0 + - - -
367C ARG* 1.3 78.8 - - - +
369C PHE* 1.3 62.2 + - - +
370C GLN* 4.1 7.3 + - - +
433C ARG* 3.1 31.5 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il